Chromophore Channeling in the G-Protein Coupled Receptor Rhodopsin

Abstract

G-protein coupled receptors (GPCRs) are transmembrane proteins that play key roles in an array of diverse biological functions, such as vision, odor, taste, and memory, and have been the targets of ca. 50% drugs on the market. However, there is very limited information on the structures of GPCRs due to the difficulty of protein purification and stability requirement of the phospholipid membrane environment. To date, the bovine rhodopsin, a light receptor protein, 1, 2 is the only GPCR whose crystal structure has been determined. Rhodopsin consists of an opsin apoprotein and an 11-cis retinal chromophore, which is covalently bonded to Lys296 via a protonated Schiff base linkage. The photoactivation cycle of rhodopsin is triggered by the cis-to-trans isomerization of retinal and ends with the release of all-trans retinal. The crystal structures show a 7-helix bundle in the transmembrane segment and that the chromophore binds in a pocket enclosed by the transmembrane helices and the β-hairpin loop connecting helix 4 and helix 5 on the extracellular surface.Despite the diverse functions, GPCRs are believed to share the 7-transmembrane helix bundle structure as in rhodopsin. Therefore, rhodopsin structure has been used as the template to model a large number of GPCR proteins, including those as drug targets. 3 Because the binding pocket is buried inside the transmembrane domain, a very interesting question is how the chromophore enters and exits the protein. This question is of great interest because understanding ligand entrance routes may help to improve drug efficacy since many of the drugs bind to the same pocket. Although the uptake and release of retinal can be detected by monitoring the intrinsic protein fluorescence, 4 direct evidence of the channeling routes is unavailable. The recent crystal structures showed no obvious channel through which the ligands can pass into the binding sites. Thus, the question regarding the paths for the uptake and release of retinal remains open.In this work, we simulated the egress of all-trans retinal from the rhodopsin protein by applying the random acceleration molecular dynamics (RAMD) method, 5 implemented by modification of the AMBER8 program.6 In the RAMD approach, a small randomly oriented force is added to the center of mass of retinal to enhance the dynamics, thus exploring the weakness of the binding pocket and allowing the retinal to exit in a computationally feasible time. The direction of the random force is kept for a certain period of time. If, during this time, retinal moves more than a certain distance, the direction of the force is maintained, otherwise a new direction is chosen randomly.The rhodopsin molecule was embedded in a phospholipid bilayer of palmitoyloleoyl phosphatidylcholine (POPC) and solvated in water. From the X-ray structure (PDB entry duan@ucdavis.edu. Supporting Information Available: Details of the system modeling and simulation. This material is available free of charge via the Internet at http://pubs.acs.org. 1U19), 2 after the simulation...

Role of Bulk Water in Hydrolysis of the Rhodopsin Chromophore

“…However, in opsin, transmembrane bundles transiently open into the hydrophobic membrane region through two holes located between helices I and VII and helices V and VI (35). A connecting channel between these openings might provide the means for retinal passage after Schiff base hydrolysis, confirming earlier predictions based on random acceleration molecular dynamics (36,37).…”

Molecular Basis of Ligand Dissociation from the Adenosine A2A Receptor

“…Such simulations have been used to study both association and dissociation of ligands to various proteins, including GPCRs (Wang and Duan, 2007;Hurst et al, 2010;Dror et al, 2011;Kruse et al, 2012). In this study, MD simulations helped us identify several amino acid residues (Table 2) that upon mutation showed a minimal effect on ZM241385's equilibrium binding affinity while having a major impact on its dissociation kinetics.…”

Crystal structure of the ligand-free G-protein-coupled receptor opsin

“…Previous biochemical experiments and molecular dynamic simulations studies have suggested that uptake and release of retinal may proceed through different gates [163,164] and Phe-276) due to movement of TM5 and TM6. A channel through the protein linking the two openings was suggested from the opsin* structure and the idea were extended by retinal docking experiments in the retinal binding site [120,165].…”